modules/genomad_endtoend

Identify mobile genetic elements present in genomic assemblies

metagenomicsgenomaddatabasedownloadphagevirusplasmid

https://github.com/nf-core/modules/[...]/modules/nf-core/genomad/endtoend

Description

Identify mobile genetic elements present in genomic assemblies

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`fasta`
`:file`

FASTA file containing contigs/scaffolds/chromosomes

*.{fasta,fna,fa}

`genomad_db`
`:directory`

Directory pointing to geNomad database

Output

name:type

description

pattern

`aggregated_classification`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_aggregated_classification/_aggregated_classification.tsv`
`:file`

Combined classification scores for each contig/scaffold/chromosome

*_aggregated_classification.tsv

`marker_classification`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_marker_classification/_marker_classification.tsv`
`:file`

Marker-based classification scores when —disable-nn-classification is used

*_marker_classification.tsv

`taxonomy`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_annotate/_taxonomy.tsv`
`:file`

Detailed output of geNomad’s marker gene taxonomy analysis

*_taxonomy.tsv

`provirus`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_find_proviruses/_provirus.tsv`
`:file`

Detailed output of each provirus identified by geNomad’s find_proviruses module

*_provirus.tsv

`compositions`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_score_calibration/_compositions.tsv`
`:file`

OPTIONAL - Predicted sample composition when --enable-score-calibration is used

*_compositions.tsv

`calibrated_classification`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_score_calibration/_calibrated_aggregated_classification.tsv`
`:file`

OPTIONAL - Classification scores that have been adjusted based on sample composition when --enable-score-calibration is used`

*_calibrated_aggregated_classification.tsv

`plasmid_fasta`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_summary/_plasmid.fna.gz`
`:file`

FASTA file containing predicted plasmid sequences

*_plasmid.fna

`plasmid_genes`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_summary/_plasmid_genes.tsv`
`:file`

TSV file containing predicted plasmid genes and their annotations

*_plasmid_genes.tsv

`plasmid_proteins`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_summary/_plasmid_proteins.faa.gz`
`:file`

FASTA file containing predicted plasmid protein sequences

*_plasmid_proteins.faa

`plasmid_summary`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_summary/_plasmid_summary.tsv`
`:file`

TSV file containing a summary of geNomad’s plasmid predictions

*_plasmid_summary.tsv

`virus_fasta`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_summary/_virus.fna.gz`
`:file`

FASTA file containing predicted virus sequences

*_virus.fna

`virus_genes`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_summary/_virus_genes.tsv`
`:file`

TSV file containing predicted virus genes and their annotations

*_virus_genes.tsv

`virus_proteins`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_summary/_virus_proteins.faa.gz`
`:file`

FASTA file containing predicted virus protein sequences

*_virus_proteins.faa

`virus_summary`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`_summary/_virus_summary.tsv`
`:file`

TSV file containing a summary of geNomad’s virus predictions

*_virus_summary.tsv

`versions_genomad`

`${task.process}`
`:string`

The name of the process

`genomad`
`:string`

The name of the tool

`genomad --version 2>&1 | sed 's/^.geNomad, version //; s/ .//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`genomad`
`:string`

The name of the tool

`genomad --version 2>&1 | sed 's/^.geNomad, version //; s/ .//'`
`:eval`

The expression to obtain the version of the tool

Tools

genomad
Lawrence Berkeley National Labs BSD variant license

Identification of mobile genetic elements

portal.nersc.gov/genomad https://github.com/apcamargo/genomad/ 10.1101/2023.03.05.531206

modules/genomad_endtoend

Description

Input

meta:map

fasta:file

genomad_db:directory

Output

aggregated_classification

meta:map

*_aggregated_classification/*_aggregated_classification.tsv:file

marker_classification

meta:map

*_marker_classification/*_marker_classification.tsv:file

taxonomy

meta:map

*_annotate/*_taxonomy.tsv:file

provirus

meta:map

*_find_proviruses/*_provirus.tsv:file

compositions

meta:map

*_score_calibration/*_compositions.tsv:file

calibrated_classification

meta:map

*_score_calibration/*_calibrated_aggregated_classification.tsv:file

plasmid_fasta

meta:map

*_summary/*_plasmid.fna.gz:file

plasmid_genes

meta:map

*_summary/*_plasmid_genes.tsv:file

plasmid_proteins

meta:map

*_summary/*_plasmid_proteins.faa.gz:file

plasmid_summary

meta:map

*_summary/*_plasmid_summary.tsv:file

virus_fasta

meta:map

*_summary/*_virus.fna.gz:file

virus_genes

meta:map

*_summary/*_virus_genes.tsv:file

virus_proteins

meta:map

*_summary/*_virus_proteins.faa.gz:file

virus_summary

meta:map

*_summary/*_virus_summary.tsv:file

versions_genomad

${task.process}:string

genomad:string

genomad --version 2>&1 | sed 's/^.*geNomad, version //; s/ .*//':eval

Topics

versions

${task.process}:string

genomad:string

genomad --version 2>&1 | sed 's/^.*geNomad, version //; s/ .*//':eval

Tools

genomad Lawrence Berkeley National Labs BSD variant license

included in

maintainers

get in touch

`meta`
`:map`

`fasta`
`:file`

`genomad_db`
`:directory`

`aggregated_classification`

`meta`
`:map`

`_aggregated_classification/_aggregated_classification.tsv`
`:file`

`marker_classification`

`meta`
`:map`

`_marker_classification/_marker_classification.tsv`
`:file`

`taxonomy`

`meta`
`:map`

`_annotate/_taxonomy.tsv`
`:file`

`provirus`

`meta`
`:map`

`_find_proviruses/_provirus.tsv`
`:file`

`compositions`

`meta`
`:map`

`_score_calibration/_compositions.tsv`
`:file`

`calibrated_classification`

`meta`
`:map`

`_score_calibration/_calibrated_aggregated_classification.tsv`
`:file`

`plasmid_fasta`

`meta`
`:map`

`_summary/_plasmid.fna.gz`
`:file`

`plasmid_genes`

`meta`
`:map`

`_summary/_plasmid_genes.tsv`
`:file`

`plasmid_proteins`

`meta`
`:map`

`_summary/_plasmid_proteins.faa.gz`
`:file`

`plasmid_summary`

`meta`
`:map`

`_summary/_plasmid_summary.tsv`
`:file`

`virus_fasta`

`meta`
`:map`

`_summary/_virus.fna.gz`
`:file`

`virus_genes`

`meta`
`:map`

`_summary/_virus_genes.tsv`
`:file`

`virus_proteins`

`meta`
`:map`

`_summary/_virus_proteins.faa.gz`
`:file`

`virus_summary`

`meta`
`:map`

`_summary/_virus_summary.tsv`
`:file`

`versions_genomad`

`${task.process}`
`:string`

`genomad`
`:string`

`genomad --version 2>&1 | sed 's/^.geNomad, version //; s/ .//'`
`:eval`

`versions`

`${task.process}`
`:string`

`genomad`
`:string`

`genomad --version 2>&1 | sed 's/^.geNomad, version //; s/ .//'`
`:eval`

genomad
Lawrence Berkeley National Labs BSD variant license